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Tikhonov S, Batin M, Gladyshev VN, Dmitriev SE, Tyshkovskiy A. AgeMeta: Quantitative Gene Expression Database of Mammalian Aging. Biochemistry (Mosc) 2024; 89:313-321. [PMID: 38622098 DOI: 10.1134/s000629792402010x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/12/2023] [Accepted: 02/13/2024] [Indexed: 04/17/2024]
Abstract
AgeMeta is a database that provides systemic and quantitative description of mammalian aging at the level of gene expression. It encompasses transcriptomic changes with age across various tissues of humans, mice, and rats, based on a comprehensive meta-analysis of 122 publicly available gene expression datasets from 26 studies. AgeMeta provides an intuitive visual interface for quantification of aging-associated transcriptomics at the level of individual genes and functional groups of genes, allowing easy comparison among various species and tissues. Additionally, all the data in the database can be downloaded and analyzed independently. Overall, this work contributes to the understanding of the complex network of biological processes underlying mammalian aging and supports future advancements in this field. AgeMeta is freely available at: https://age-meta.com/.
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Affiliation(s)
- Stanislav Tikhonov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | | | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Alexander Tyshkovskiy
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Rafikova E, Nemirovich-Danchenko N, Ogmen A, Parfenenkova A, Velikanova A, Tikhonov S, Peshkin L, Rafikov K, Spiridonova O, Belova Y, Glinin T, Egorova A, Batin M. Open Genes-a new comprehensive database of human genes associated with aging and longevity. Nucleic Acids Res 2024; 52:D950-D962. [PMID: 37665017 PMCID: PMC10768108 DOI: 10.1093/nar/gkad712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/31/2023] [Accepted: 08/19/2023] [Indexed: 09/05/2023] Open
Abstract
The Open Genes database was created to enhance and simplify the search for potential aging therapy targets. We collected data on 2402 genes associated with aging and developed convenient tools for searching and comparing gene features. A comprehensive description of genes has been provided, including lifespan-extending interventions, age-related changes, longevity associations, gene evolution, associations with diseases and hallmarks of aging, and functions of gene products. For each experiment, we presented the necessary structured data for evaluating the experiment's quality and interpreting the study's findings. Our goal was to stay objective and precise while connecting a particular gene to human aging. We distinguished six types of studies and 12 criteria for adding genes to our database. Genes were classified according to the confidence level of the link between the gene and aging. All the data collected in a database are provided both by an API and a user interface. The database is publicly available on a website at https://open-genes.org/.
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Affiliation(s)
- Ekaterina Rafikova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Nikolay Nemirovich-Danchenko
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
- Faculty of Cytology and Genetics, National Research Tomsk State University, Tomsk 634050, Russia
| | - Anna Ogmen
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Anna Parfenenkova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | | | - Stanislav Tikhonov
- Faculty of Bioengineering and Bioinformatics, Moscow State University, Moscow 119991, Russia
| | - Leonid Peshkin
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Konstantin Rafikov
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Olga Spiridonova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Yulia Belova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Timofey Glinin
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
- Endocrine Neoplasia Laboratory, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Department of Genetics & Biotechnology, Saint Petersburg State University, Saint Petersburg 199034, Russia
| | - Anastasia Egorova
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
| | - Mikhail Batin
- Open Longevity, 15260 Ventura Blvd, STE 2230, Sherman Oaks, CA 91403, USA
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